Abstract 6082: Assessing difference in the tumor and immune microenvironment of BRCA1/2 mutated versus BRCA wild type high grade serous ovarian cancers
Authors: Jing Qian, Lynda D. Roman, Seeta Rajpara, Monica Neuman, Varun Khetan, David W. Craig, Joseph Carlson, John D. Carpten
Journal: Cancer Research (2023)

Abstract Ovarian cancer (OvCa) is the deadliest gynecological malignancy in the United States. Surgery and chemotherapy are the primary treatments for OvCa, but 80% of late-stage OvCa patients experience chemo-resistant recurrence, which necessitates the development of new treatment strategies. The genomic diversity within a tumor and the interactions among various cell types within its microenvironment are considered key factors contributing to therapeutic efficacy. Specifically, women who harbor germline BRCA1 or BRCA2 mutations are at increased risk of developing high grade serous ovarian cancer (HGSC). To understand the genomic consequences, including somatic alterations, associated with defective DNA repair, tumor DNA and RNA was isolated from fresh frozen OCT embedded sections from 15 HGSC patients with BRCA1/2 mutation and 10 without any alterations in the BRCA genes (BRCA-wt). Whole exome sequencing (WES) and total RNA-seq was performed to determine the association of homologous recombination (HR) DNA repair gene defects with tumor mutation burden (TMB), neoantigen load (NL), and immunological assessment of tumor microenvironment. TMB was calculated from mutation rates of somatic WES. Germline exome analysis was used to validate inherited BRCA mutations. To identify the somatic mutations, somatic single nucleotide variants and InDels were detected using Strelka. TP53 mutations were most common with several other genes showing only modest mutation frequency. Mutation signatures were also detected with maftools and compared to the COSMIC mutational signature database. BRCA-mutated samples displayed a unique mutational signature associated with defects in HR DNA repair pathway. We also observed heterogeneity in copy number variation profiles amongst cases, as determined by the tool Sequenza. Furthermore, gene set enrichment analysis indicated differential enrichment of P53 pathway, MAPK pathway, and PTEN pathway, in addition to numerous pathways related to immune cell signaling and immune response. RNA-seq data was analyzed with CIBERSORTx and revealed different proportions of 22 immune effector cell types that accompany tumor cells within the HGSC microenvironment. Additional analyses are underway, including measuring differences in NL in BRCA-mutated versus BRCA-wt cases. This work will represent a significant advancement in our fundamental knowledge regarding the complexities of the TME and effective immunological responses in OvCa. Citation Format: Jing Qian, Lynda D. Roman, Seeta Rajpara, Monica Neuman, Varun Khetan, David W. Craig, Joseph Carlson, John D. Carpten. Assessing difference in the tumor and immune microenvironment of BRCA1/2 mutated versus BRCA wild type high grade serous ovarian cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6082.